SEC22C

Summary

SEC22C (SEC22 homolog C, vesicle trafficking protein, HGNC:16828) is a protein-coding gene on chromosome 3p22.1, encoding Vesicle-trafficking protein SEC22c (Q9BRL7). May be involved in vesicle transport between the ER and the Golgi complex.

This gene encodes a member of the SEC22 family of vesicle trafficking proteins. The encoded protein is localized to the endoplasmic reticulum and may play a role in the early stages of ER-Golgi protein trafficking. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene.

Source: NCBI Gene 9117 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 62 total
• MANE Select transcript: NM_032970

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16828
Approved symbol	SEC22C
Name	SEC22 homolog C, vesicle trafficking protein
Location	3p22.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC13261, MGC5373
Ensembl gene	ENSG00000093183
Ensembl biotype	protein_coding
OMIM	604028
Entrez	9117

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 13 protein_coding, 4 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000264454, ENST00000273156, ENST00000383750, ENST00000416880, ENST00000417572, ENST00000420163, ENST00000423701, ENST00000445388, ENST00000449617, ENST00000450981, ENST00000451653, ENST00000454141, ENST00000456222, ENST00000456515, ENST00000487701, ENST00000493107, ENST00000908028, ENST00000908029, ENST00000915686, ENST00000970522

RefSeq mRNA: 4 — MANE Select: NM_032970 NM_001201572, NM_001201584, NM_004206, NM_032970

CCDS: CCDS2699, CCDS2700, CCDS56246

Canonical transcript exons

ENST00000264454 — 7 exons

Exon	Start	End
ENSE00001684949	42547969	42553448
ENSE00003558036	42557578	42557696
ENSE00003563153	42563523	42563686
ENSE00003570836	42555930	42555995
ENSE00003649863	42561117	42561296
ENSE00003675268	42568865	42569073
ENSE00003848613	42581846	42581967

Expression profiles

Bgee: expression breadth ubiquitous, 260 present calls, max score 95.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 35.2661 / max 149.3429, expressed in 1821 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
41788	30.1248	1817
41787	2.4766	1388
41791	1.7735	669
41792	0.4516	260
41793	0.4396	230

Top tissues by expression

262 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
parotid gland	UBERON:0001831	95.93	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	95.44	gold quality
spinal cord	UBERON:0002240	95.28	gold quality
mucosa of stomach	UBERON:0001199	94.42	gold quality
jejunal mucosa	UBERON:0000399	94.41	gold quality
popliteal artery	UBERON:0002250	94.24	gold quality
tibial artery	UBERON:0007610	94.24	gold quality
artery	UBERON:0001637	94.07	gold quality
subthalamic nucleus	UBERON:0001906	93.99	gold quality
right lung	UBERON:0002167	93.96	gold quality
right coronary artery	UBERON:0001625	93.94	gold quality
adult organism	UBERON:0007023	93.89	gold quality
tibial nerve	UBERON:0001323	93.80	gold quality
descending thoracic aorta	UBERON:0002345	93.72	gold quality
aorta	UBERON:0000947	93.68	gold quality
substantia nigra	UBERON:0002038	93.47	gold quality
left coronary artery	UBERON:0001626	93.45	gold quality
islet of Langerhans	UBERON:0000006	93.37	gold quality
seminal vesicle	UBERON:0000998	93.20	gold quality
midbrain	UBERON:0001891	93.17	gold quality
ileal mucosa	UBERON:0000331	93.16	gold quality
endothelial cell	CL:0000115	93.11	gold quality
upper arm skin	UBERON:0004263	93.11	gold quality
pons	UBERON:0000988	93.01	gold quality
smooth muscle tissue	UBERON:0001135	93.00	gold quality
coronary artery	UBERON:0001621	93.00	gold quality
thoracic aorta	UBERON:0001515	92.99	gold quality
ascending aorta	UBERON:0001496	92.92	gold quality
superficial temporal artery	UBERON:0001614	92.61	gold quality
substantia nigra pars reticulata	UBERON:0001966	92.59	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

95 targeting SEC22C, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-8068	99.98	73.85	2376
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-8075	99.97	67.20	962
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488

Literature-anchored findings (GeneRIF, showing 1)

• These results indicate that the splicing-dependent changes in the number of TMDs allow Sec22c to regulate the subcellular localization in cooperation with ARF4, implying that Sec22c will function at the Golgi as well as the ER. (PMID:28414125)

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	sec22c	ENSDARG00000063387
mus_musculus	Sec22c	ENSMUSG00000061536
rattus_norvegicus	Sec22c	ENSRNOG00000086885
drosophila_melanogaster	Syb	FBGN0003660
caenorhabditis_elegans		WBGENE00004898
caenorhabditis_elegans		WBGENE00004899
caenorhabditis_elegans		WBGENE00014084
caenorhabditis_elegans		WBGENE00044062

Paralogs (10): VAMP3 (ENSG00000049245), YKT6 (ENSG00000106636), VAMP4 (ENSG00000117533), VAMP8 (ENSG00000118640), SEC22A (ENSG00000121542), VAMP7 (ENSG00000124333), VAMP1 (ENSG00000139190), VAMP5 (ENSG00000168899), VAMP2 (ENSG00000220205), SEC22B (ENSG00000265808)

Protein

Protein identifiers

Vesicle-trafficking protein SEC22c — Q9BRL7 (reviewed: Q9BRL7)

Alternative names: SEC22 vesicle-trafficking protein homolog C, SEC22 vesicle-trafficking protein-like 3

All UniProt accessions (10): Q9BRL7, A0A024R2N5, C9J2R1, C9J448, C9J9A4, C9JNW1, F8VQT7, F8WBN1, F8WDR5, H7C479

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in vesicle transport between the ER and the Golgi complex.

Subcellular location. Endoplasmic reticulum membrane.

Tissue specificity. Ubiquitously expressed.

Similarity. Belongs to the synaptobrevin family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9BRL7-1	1	yes
Q9BRL7-2	2
Q9BRL7-3	3

RefSeq proteins (4): NP_001188501, NP_001188513, NP_004197, NP_116752* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010908	Longin_dom	Domain
IPR011012	Longin-like_dom_sf	Homologous_superfamily
IPR043546	Sec22a/c	Family
IPR059071	SEC22a-c_C	Domain

Pfam: PF13774, PF25970

UniProt features (15 total): topological domain 5, splice variant 4, transmembrane region 4, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BRL7-F1	82.85	0.52

Function

Pathways and Gene Ontology

Reactome pathways

8 pathways

ID	Pathway
R-HSA-204005	COPII-mediated vesicle transport
R-HSA-199977	ER to Golgi Anterograde Transport
R-HSA-199991	Membrane Trafficking
R-HSA-392499	Metabolism of proteins
R-HSA-446203	Asparagine N-linked glycosylation
R-HSA-5653656	Vesicle-mediated transport
R-HSA-597592	Post-translational protein modification
R-HSA-948021	Transport to the Golgi and subsequent modification

MSigDB gene sets: 176 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_UP, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, TERAMOTO_OPN_TARGETS_CLUSTER_3, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, chr3p22, GCM_NUMA1, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, FISCHER_DREAM_TARGETS, GCM_NF2, ZHANG_BREAST_CANCER_PROGENITORS_UP, MODULE_342, NUYTTEN_EZH2_TARGETS_DN, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK

GO Biological Process (3): endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), protein transport (GO:0015031), vesicle-mediated transport (GO:0016192)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (4): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-7 pathways:

Category	Pathways
ER to Golgi Anterograde Transport	1
Membrane Trafficking	1
Transport to the Golgi and subsequent modification	1
Vesicle-mediated transport	1
Post-translational protein modification	1
Metabolism of proteins	1
Asparagine N-linked glycosylation	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	2
transport	2
cellular anatomical structure	2
intercellular transport	1
intracellular transport	1
Golgi vesicle transport	1
intracellular protein localization	1
establishment of protein localization	1
cellular process	1
binding	1
endomembrane system	1
intracellular membrane-bounded organelle	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1110 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SEC22C	GOSR2	O14653	876
SEC22C	BET1	O15155	871
SEC22C	STX5	Q13190	751
SEC22C	VTI1B	Q9UEU0	702
SEC22C	ZC2HC1B	Q5TFG8	666
SEC22C	FAM163B	P0C2L3	645
SEC22C	SS18L2	Q9UHA2	570
SEC22C	GOLPH3	Q9H4A6	545
SEC22C	ZDHHC22	Q8N966	542
SEC22C	GOSR1	O95249	506
SEC22C	YKT6	O15498	501
SEC22C	FAM169A	Q9Y6X4	480
SEC22C	CRISPLD1	Q9H336	470
SEC22C	VAMP7	P51809	465
SEC22C	BET1L	Q9NYM9	437

IntAct

19 interactions, top by confidence:

A	B	Type	Score
FATE1	SEC22C	psi-mi:“MI:0915”(physical association)	0.720
SEC22C	FATE1	psi-mi:“MI:0915”(physical association)	0.720
ZSCAN29	SEC22C	psi-mi:“MI:0915”(physical association)	0.560
GJA8	SEC22C	psi-mi:“MI:0915”(physical association)	0.560
SEC22C	LIME1	psi-mi:“MI:0915”(physical association)	0.560
SEC22C	CFTR	psi-mi:“MI:0915”(physical association)	0.370
CFTR	SEC22C	psi-mi:“MI:0915”(physical association)	0.370
SEC22C	ACADS	psi-mi:“MI:0914”(association)	0.350
SEC22C	ZSCAN29	psi-mi:“MI:0915”(physical association)	0.000
SEC22C	GJA8	psi-mi:“MI:0915”(physical association)	0.000
SEC22C	LIME1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (25): FATE1 (Two-hybrid), ABAT (Affinity Capture-MS), HK3 (Affinity Capture-MS), ACADS (Affinity Capture-MS), SERPINA12 (Affinity Capture-MS), POLG2 (Affinity Capture-MS), IL1RN (Affinity Capture-MS), HK3 (Affinity Capture-MS), IL1RN (Affinity Capture-MS), ACADS (Affinity Capture-MS), SERPINA12 (Affinity Capture-MS), POLG2 (Affinity Capture-MS), ABAT (Affinity Capture-MS), FATE1 (Two-hybrid), GJA8 (Two-hybrid)

ESM2 similar proteins: A0A140LIJ0, A1L1L2, A3KN46, A4FV45, A9ULG4, B1H1N7, O95202, P0C1Q3, P0DKR2, P82933, Q0VCA3, Q149M9, Q14CZ7, Q1LXZ7, Q28EM8, Q2TBP8, Q3B8B2, Q3SZK4, Q3U2U7, Q4V8A1, Q58CX2, Q5M9G9, Q5PQQ5, Q5T197, Q5T1A1, Q5XIN6, Q5ZJY9, Q640M6, Q66JZ4, Q6DJ55, Q6NUQ4, Q6P1Q0, Q6PA48, Q6PBN5, Q6ZQE4, Q7TNU7, Q7YS91, Q810S1, Q86VS3, Q8BM55

Diamond homologs: O08547, O08595, O75396, P22214, Q4KM74, Q4R866, Q5RAI9, Q5ZJW4, Q642F4, Q6C880, Q6CJA0, Q6FWT0, Q6P7L4, Q74ZD2, Q7SXP0, Q7ZV15, Q8BH47, Q8BXT9, Q94AU2, Q96IW7, Q9BRL7, Q9Y7L0, Q2YDJ2, O60073, O70404, P36015

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

62 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	40
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2309 predictions. Top by Δscore:

Variant	Effect	Δscore
3:42557693:GGAG:G	acceptor_gain	1.0000
3:42557697:C:CC	acceptor_gain	1.0000
3:42557700:CACAA:C	acceptor_gain	1.0000
3:42557702:CAA:C	acceptor_gain	1.0000
3:42557703:A:T	acceptor_gain	1.0000
3:42557704:A:AC	acceptor_gain	1.0000
3:42557704:A:C	acceptor_gain	1.0000
3:42561112:CTTA:C	donor_loss	1.0000
3:42561113:TTAC:T	donor_loss	1.0000
3:42561114:TA:T	donor_loss	1.0000
3:42561115:A:AC	donor_gain	1.0000
3:42561115:AC:A	donor_gain	1.0000
3:42561115:ACC:A	donor_loss	1.0000
3:42561116:C:CT	donor_gain	1.0000
3:42561116:CC:C	donor_gain	1.0000
3:42561116:CCA:C	donor_gain	1.0000
3:42561116:CCAG:C	donor_gain	1.0000
3:42561116:CCAGG:C	donor_gain	1.0000
3:42561293:CTGT:C	acceptor_gain	1.0000
3:42561294:TGT:T	acceptor_gain	1.0000
3:42561296:TCTG:T	acceptor_loss	1.0000
3:42561297:C:CC	acceptor_gain	1.0000
3:42561298:T:C	acceptor_loss	1.0000
3:42563522:CCAAA:C	donor_gain	1.0000
3:42563526:A:C	donor_gain	1.0000
3:42563541:ATGG:A	donor_gain	1.0000
3:42568863:A:AC	donor_gain	1.0000
3:42568864:C:CC	donor_gain	1.0000
3:42568897:TCG:T	donor_gain	1.0000
3:42590963:GCGG:G	donor_gain	1.0000

AlphaMissense

1997 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:42563524:A:C	F115L	0.986
3:42563524:A:T	F115L	0.986
3:42563526:A:G	F115L	0.986
3:42555960:A:C	F227L	0.984
3:42555960:A:T	F227L	0.984
3:42555962:A:G	F227L	0.984
3:42557631:A:G	C198R	0.983
3:42557617:A:C	N202K	0.981
3:42557617:A:T	N202K	0.981
3:42563587:G:C	F94L	0.981
3:42563587:G:T	F94L	0.981
3:42563589:A:G	F94L	0.981
3:42563588:A:G	F94S	0.977
3:42568994:A:T	L18H	0.977
3:42553350:C:A	R270S	0.973
3:42553350:C:G	R270S	0.973
3:42553448:A:G	C238R	0.973
3:42557615:A:G	L203P	0.971
3:42569000:A:G	L16P	0.970
3:42553284:C:A	R292S	0.969
3:42553284:C:G	R292S	0.969
3:42557607:C:G	G206R	0.968
3:42557607:C:T	G206R	0.968
3:42553351:C:A	R270M	0.967
3:42563611:G:C	F86L	0.967
3:42563611:G:T	F86L	0.967
3:42563613:A:G	F86L	0.967
3:42553351:C:G	R270T	0.966
3:42557629:A:C	C198W	0.966
3:42563617:G:C	F84L	0.966

dbSNP variants (sampled 300 via entrez): RS1000031355 (3:42587536 G>A), RS1000047793 (3:42594248 G>C), RS1000079707 (3:42570638 G>A), RS1000115352 (3:42589997 C>G,T), RS1000183047 (3:42591523 A>G,T), RS1000189937 (3:42581282 T>C), RS1000219315 (3:42590503 T>C), RS1000221006 (3:42581581 T>C), RS1000270115 (3:42597176 A>G,T), RS1000287438 (3:42551378 G>A,T), RS1000302596 (3:42597415 G>A,T), RS1000384532 (3:42558597 G>C), RS1000389281 (3:42600621 C>A), RS1000405124 (3:42573963 A>G), RS1000415752 (3:42558263 G>A)

Disease associations

OMIM: gene MIM:604028 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST010988_137	Adult body size	4.000000e-09

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects expression, decreases expression, affects cotreatment	5
Air Pollutants	increases abundance, decreases expression, affects expression	2
Nickel	increases expression	2
Aflatoxin B1	decreases methylation	2
Particulate Matter	decreases expression, increases abundance, affects expression	2
triphenyl phosphate	affects expression	1
methylparaben	decreases expression	1
sodium arsenite	affects splicing, decreases expression	1
potassium chromate(VI)	decreases expression	1
beta-methylcholine	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Acetaminophen	increases expression	1
Vehicle Emissions	affects expression, increases abundance	1
Diethylstilbestrol	increases expression	1
Estradiol	increases expression	1
Formaldehyde	decreases expression	1
Ozone	affects expression, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1
Sodium Dodecyl Sulfate	increases expression	1
Tretinoin	decreases expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	decreases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_TK34	HAP1 SEC22C (-) 1	Cancer cell line	Male
CVCL_TK35	HAP1 SEC22C (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.